Re: [GRASS-dev] openMP support in GRASS GIS
Hi, yes I already changed the r.sim.sediment, so it is running there, I just wanted to check there is no theoretical issue since you haven't mentioned it in the paper. I kept the max number of walkers lower as it was, the problem if I remember correctly is that is uses static allocations, so if we raise it, it will take a lot of memory. So that would need to be rewritten. Perhaps you should create a ticket about that error, to keep track of it. Thank you On Thu, Aug 24, 2017 at 3:38 PM, Jaro Hofierka wrote: > Hi Anna, > > many thanks! Please keep it in addons for a while, as it is referenced in > the paper. Yes it is possible to use it in r.sim.sediment as well because > actually we have parallelized the simulation library (simlib) used by > r.sim.sediment as well. But it needs some modification of Makefile and > main.c to include openMP. Otherwise it runs without OpenMP. > Also please note that I have changed the maximum number of walkers in > waterglobs.h to 20 million from 7 million. This might be needed to compute > large grids, but the simulation algorithm should be checked because > sometimes it reports error (nwalk > maxw) when assigns walkers (this is not > related to openMP). > > Best wishes, > > Jaro > > Anna Petrášová napísal(a): > >> Dear Jaro and all, >> >> During recent code sprint in Boston I ported r.sim.water.mp to GRASS >> r.sim.water and r.sim.sediment. I tested it with r.sim.sediment and it >> seems to work, so let me know if there are any reasons parallelization >> shouldn't be used with r.sim.sediment. I removed all the commented >> parts which you probably put there during experimenting. I didn't >> remove the version in addons, because you have it linked in your >> paper, but maybe we should put a note in the r.sim.water.mp manual, >> that the latest version is in the core? As for r.sun, when I have >> time, I will look at it. >> >> Anna >> >> On Sat, Aug 5, 2017 at 4:24 AM, Jaro Hofierka wrote: >>> >>> Hi Markus, >>> >>> This is just a small contribution and I would like acknowledge help of >>> reviewers to improve the manuscript. I believe more such grass-based >>> papers >>> in scientific journals will further promote GRASS within the wider >>> scientific community. >>> Of course, we would welcome if this could go to the trunk version. Vaclav >>> helped us is v.surf.rst and it is already there and I hope he could also >>> help with r.sim.water and r.sun. He can contact me or my colleagues and >>> we >>> will provide any assistance. >>> >>> Best wishes, >>> >>> Jaro >>> >>> Markus Neteler napísal(a): >>> Hi, just saw that this article got published (congrats, Jaro and team): Hofierka, J., Lacko, M., Zubal, S., 2017. Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP. Computers & Geosciences. doi:10.1016/j.cageo.2017.07.007 Questions: since the code is already in addons, how about merging the changes into trunk? Markus >>> ___ >>> grass-dev mailing list >>> grass-dev@lists.osgeo.org >>> https://lists.osgeo.org/mailman/listinfo/grass-dev >> >> > ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] openMP support in GRASS GIS
Hi Anna, many thanks! Please keep it in addons for a while, as it is referenced in the paper. Yes it is possible to use it in r.sim.sediment as well because actually we have parallelized the simulation library (simlib) used by r.sim.sediment as well. But it needs some modification of Makefile and main.c to include openMP. Otherwise it runs without OpenMP. Also please note that I have changed the maximum number of walkers in waterglobs.h to 20 million from 7 million. This might be needed to compute large grids, but the simulation algorithm should be checked because sometimes it reports error (nwalk > maxw) when assigns walkers (this is not related to openMP). Best wishes, Jaro Anna Petrášová napísal(a): Dear Jaro and all, During recent code sprint in Boston I ported r.sim.water.mp to GRASS r.sim.water and r.sim.sediment. I tested it with r.sim.sediment and it seems to work, so let me know if there are any reasons parallelization shouldn't be used with r.sim.sediment. I removed all the commented parts which you probably put there during experimenting. I didn't remove the version in addons, because you have it linked in your paper, but maybe we should put a note in the r.sim.water.mp manual, that the latest version is in the core? As for r.sun, when I have time, I will look at it. Anna On Sat, Aug 5, 2017 at 4:24 AM, Jaro Hofierka wrote: Hi Markus, This is just a small contribution and I would like acknowledge help of reviewers to improve the manuscript. I believe more such grass-based papers in scientific journals will further promote GRASS within the wider scientific community. Of course, we would welcome if this could go to the trunk version. Vaclav helped us is v.surf.rst and it is already there and I hope he could also help with r.sim.water and r.sun. He can contact me or my colleagues and we will provide any assistance. Best wishes, Jaro Markus Neteler napísal(a): Hi, just saw that this article got published (congrats, Jaro and team): Hofierka, J., Lacko, M., Zubal, S., 2017. Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP. Computers & Geosciences. doi:10.1016/j.cageo.2017.07.007 Questions: since the code is already in addons, how about merging the changes into trunk? Markus ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] openMP support in GRASS GIS
Dear Jaro and all, During recent code sprint in Boston I ported r.sim.water.mp to GRASS r.sim.water and r.sim.sediment. I tested it with r.sim.sediment and it seems to work, so let me know if there are any reasons parallelization shouldn't be used with r.sim.sediment. I removed all the commented parts which you probably put there during experimenting. I didn't remove the version in addons, because you have it linked in your paper, but maybe we should put a note in the r.sim.water.mp manual, that the latest version is in the core? As for r.sun, when I have time, I will look at it. Anna On Sat, Aug 5, 2017 at 4:24 AM, Jaro Hofierka wrote: > Hi Markus, > > This is just a small contribution and I would like acknowledge help of > reviewers to improve the manuscript. I believe more such grass-based papers > in scientific journals will further promote GRASS within the wider > scientific community. > Of course, we would welcome if this could go to the trunk version. Vaclav > helped us is v.surf.rst and it is already there and I hope he could also > help with r.sim.water and r.sun. He can contact me or my colleagues and we > will provide any assistance. > > Best wishes, > > Jaro > > Markus Neteler napísal(a): > >> Hi, >> >> just saw that this article got published (congrats, Jaro and team): >> >> Hofierka, J., Lacko, M., Zubal, S., 2017. Parallelization of >> interpolation, solar radiation and water flow simulation modules in >> GRASS GIS using OpenMP. Computers & Geosciences. >> doi:10.1016/j.cageo.2017.07.007 >> >> Questions: since the code is already in addons, how about merging the >> changes into trunk? >> >> Markus >> > ___ > grass-dev mailing list > grass-dev@lists.osgeo.org > https://lists.osgeo.org/mailman/listinfo/grass-dev ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] openMP support in GRASS GIS
Hi Markus, This is just a small contribution and I would like acknowledge help of reviewers to improve the manuscript. I believe more such grass-based papers in scientific journals will further promote GRASS within the wider scientific community. Of course, we would welcome if this could go to the trunk version. Vaclav helped us is v.surf.rst and it is already there and I hope he could also help with r.sim.water and r.sun. He can contact me or my colleagues and we will provide any assistance. Best wishes, Jaro Markus Neteler napísal(a): Hi, just saw that this article got published (congrats, Jaro and team): Hofierka, J., Lacko, M., Zubal, S., 2017. Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP. Computers & Geosciences. doi:10.1016/j.cageo.2017.07.007 Questions: since the code is already in addons, how about merging the changes into trunk? Markus ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] openMP support in GRASS GIS
Thanks Maris, [BTW: your mail was sent only to me, so I'm forwarding to the list.] On 04/08/17 16:04, Maris Nartiss wrote: 1. It is not a dependency, as OpenMP code should run just fine also when compiled without OpenMP. Those are just comments in code thus backwards safe. Right. I now see that all code is conditionalized on _OPENMP being set and I suppose that happens when you use --with-openmp as a compiler switch ? 2. It is not as easy as it seems, as every place, where parallelisation is introduced, needs to be examined carefully to not introduce hard to track issues when common variables are changed and to not make even worse performance by making CPU cache dirty when it isn't. Of course these problems affect only binaries compiled with OpenMP. Thus OpenMP support in GRASS GIS could be marked as "use at own risk". This thus means that merging the OpenMP version into the trunk version will not have any consequences for the "normal" user. However, does it mean that maintenance of the modules will become more complex ? I see that in v.surf.rst the OpenMP stuff has already been integrated. It's only been 7 months, but up to now noone has complained, so I think we could integrate openmp into the two other modules as well (r.sun + r.sim.water). Moritz ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] openMP support in GRASS GIS
On 04/08/17 12:35, Markus Neteler wrote: Hi, just saw that this article got published (congrats, Jaro and team): Hofierka, J., Lacko, M., Zubal, S., 2017. Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP. Computers & Geosciences. doi:10.1016/j.cageo.2017.07.007 Questions: since the code is already in addons, how about merging the changes into trunk? I'm no expert on OpenMP. I imagine it is integrated at compile time ? does this mean that openmp will become a dependency of GRASS GIS ? Moritz ___ grass-dev mailing list grass-dev@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-dev
